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7. Nextflow pipeline outputs

7. Nextflow pipeline outputs

Owned by Marie-Emilie Gauthier
Last updated: Sept 27, 2024
1 min read

Results folder

The results are output in the folder name specified in the .nexftlow.config file under the outdir parameter. It is generally set to be results.

params { outdir = 'results' }

Nextflow log, metrics and reports

By default, Nextflow will create a log file in the working directory called .nextflow.log. This file is hidden but you can see it using the command:

ls -a

If you rerun the pipeline in the same folder, the previous .nextflow.log will be renamed .nextflow.log.1 and a new .nextflow.log will be generated.

You can change the default location by specifying a different location

nextflow -log ~/code/nextflow.log run

You can list the execution logs of previous invocations of all pipelines in a directory by running the command:

nextflow log
TIMESTAMP DURATION RUN NAME STATUS REVISION ID SESSION ID COMMAND 2024-09-23 15:38:11 27m 5s cranky_pike OK 5901bea438 449030e3-e32d-4010-bc1c-9d6f1f62cc45 nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.3.1 2024-09-24 14:18:37 1m 45s agitated_bose OK 5901bea438 449030e3-e32d-4010-bc1c-9d6f1f62cc45 nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.3.1 -resume --multiqc_title smrnaseq

If we want to get more information about an individual run we can add the run name or session ID to the log command.

For example:

nextflow log agitated_bose
/mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/d5/fd4b1581fd60a640f586ca9557e425 /mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/20/88bac48f8031d973e7d47e215baf73 /mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/6d/427866552c311523327e16d3ec0b32 /mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/c0/aa328b61d23c7f1ca738aa5f5fc142 /mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/b5/3e73ab56f65b707a1db9767ce472ea /mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/aa/35a63e37a55434920fc7f3e4a99c80 /mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/95/6d0db42195231bb9861871c7700798 ...

Generate an html run report

cat <<EOF > my_template.html <div> <h2>\${name}</h2> <div> Script: <pre>\${script}</pre> </div> <ul> <li>Exit: \${exit}</li> <li>Status: \${status}</li> <li>Work dir: \${workdir}</li> <li>Container: \${container}</li> </ul> </div> EOF

Run the following command:

nextflow log agitated_bose -t template.html > nextflow_run_report.html

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